The goal of education is to cultivate students’ innovative spirit, innovative thinking and innovative ability. Natural pharmaceutical chemistry is a required course for pharmacy majors, and plays an important role in the pharmaceutical courses. In order to meet the requirements of the society for innovative talents in pharmacy, this project, based on the teaching characteristics of the course “Natural Pharmaceutical Chemistry”, combined with scientific research, explored and studied the teaching of natural pharmaceutical chemistry, and explored the ways and specific methods to cultivate students’ innovation ability from the aspects of theoretical teaching, experimental teaching, graduation practice and undergraduate thesis design. The improvement of students’ innovation ability plays an important role in promoting teaching work, improving teaching quality and students’ employment level. With the deepening of the reform of higher education, we will also continue to explore new ideas, new ways and new measures that are conducive to pharmaceutical education, so that the teaching level of natural pharmaceutical chemistry will continue to improve and students’ innovation ability will continue to strengthen.